Background: In mungbean crop, the yield gap in many high yielding varieties is mainly due to lack of resistance to pre-harvest sprouting and wetting due to rains at physiological maturity or just before harvesting. Prevention of pre-harvest sprouting damage forms the most important challenge in mungbean since it has been identified as the crucial constraint for improving seed yield and quality seed. With the above perspective, the present study is aimed to identify morpho-physiological features responsible for pre-harvest sprouting and to reveal ultra structural architecture of pod and seeds of mungbean genotypes, imparting susceptibility or tolerance to pre-harvest sprouting. Methods: Four mungbean genotypes viz. ML 267 and MGG 295 (susceptible) and LGG 450 and K 851 (tolerant) were used to study the details of morpho-physiological characters such as: layers and thickness of podwall, seed coat, their external surface and internal structures of seed using scanning electron microscopy. The quantity of water accumulated, rate of moisture absorption, speed, path and pattern of water movement across the podwall and seed coat including locular space, cotyledonary area and embryonic region were studied using I2-KI treated water in time course studies on water pathway. Result: The ultrastructural architecture of pod, morpho-physiological features endowed with differential biomolecular alignment together determine the trait of tolerance or susceptibility to pre-harvest sprouting in mungbean genotypes.